Evidence map›Paper›PMID 40294103›Full record

ArticleMicrobial genomics2025

Integrated population clustering and genomic epidemiology with PopPIPE.

Martin P McHugh, Samuel T Horsfield, Johanna von Wachsmann, Jacqueline Toussaint, Kerry A Pettigrew, Elzbieta Czarniak, Thomas J Evans, Alistair Leanord, Luke Tysall, Stephen H Gillespie and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbial genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Novel transposon TnMicrobial genomics · 2026
    Article
  2. Novel transposon TnmedRxiv : the preprint server for health sciences · 2026
    Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Martin P McHughMedical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Samuel T HorsfieldEuropean Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK.
Johanna von WachsmannEuropean Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK.
Jacqueline ToussaintEuropean Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK.
Kerry A PettigrewMedical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Elzbieta CzarniakMedical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Thomas J EvansSchool of Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK.
Alistair LeanordSchool of Infection and Immunity, University of Glasgow, Glasgow G12 8QQ, UK.
Luke TysallMedical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Stephen H GillespieDivision of Infection and Global Health, University of St Andrews, St Andrews KY16 9AJ, UK.
Kate E TempletonMedical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK.
Matthew T G HoldenDivision of Infection and Global Health, University of St Andrews, St Andrews KY16 9AJ, UK.
Nicholas J CroucherMRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London SW7 2AZ, UK.
John A LeesEuropean Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, UK.

Funding

Penn State Clinical and Translational Science InstituteKL2TR000126 · NCATS · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI SINOWAY, LAWRENCE I · 2012 to 2015
$3.2M
NCATS NIH HHS KL2 TR000126
6 · The paper itself

Abstract

Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive detection of genetic differences, especially among closely related samples found in outbreaks. However, across longer genetic distances, frequent recombination can make calculation and interpretation of these differences more challenging, requiring significant bioinformatic expertise and manual intervention during the analysis process. Here, we present a

Indexed as

Genome, BacterialGenomicsStreptococcus pneumoniaeCluster AnalysisComputational BiologyCross InfectionEnterococcus faeciumHumansMolecular EpidemiologyMultilocus Sequence TypingPhylogenyclusteringgenomic epidemiologypipelinestransmission

Identifiers

PMID40294103
PMCPMC12038005

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.